Wave function analysis of MHC-peptide interactions

Constanza Cárdenas, Mateo Obregón, Alejandro Balbín, José Luis Villaveces, Manuel E Patarroyo

    Research output: Contribution to journalArticle

    5 Citations (Scopus)

    Abstract

    We have carried out an analysis of the wave function data for three MHC-peptide complexes: HLA-DR beta 1*0101-HA, HLA-DR beta 1*0401-HA and HLA-DR beta 1*0401-Col. We used quantum chemistry computer programs to generate wave function coefficients for these complexes, from which we obtained both molecular and atomic orbital data for both pocket and peptide amino acids within each pocket region. From these discriminated data, interaction molecular orbitals (IMOs) were identified as those with large and similar atomic orbital coefficient contributions from both pocket and peptide amino acids. The present results correlate well with our previous research where only electrostatic moments were used to explore molecular component interactions. Furthermore, we show a quantum chemical methodology to produce more fine-grained results concerning amino acid behavior in the MHC-peptide interaction. (c) 2006 Elsevier Inc. All rights reserved.

    Original languageEnglish
    Pages (from-to)605-615
    Number of pages11
    JournalJournal of Molecular Graphics and Modelling
    Volume25
    Issue number5
    DOIs
    Publication statusPublished - Jan 2007

    Keywords

    • molecular interactions
    • molecular orbital coefficients
    • MHC pockets
    • theoretical study of MHC
    • T-CELL EPITOPES
    • CLASS-II MOLECULE
    • PROTEIN DATA-BANK
    • HLA-DR4 DRA-ASTERISK-0101
    • HEMAGGLUTININ PEPTIDE
    • CRYSTAL-STRUCTURE
    • HLA-DR-BETA-1-ASTERISK-0101-HA
    • DRB1-ASTERISK-0401
    • COMPLEXES

    Cite this

    Cárdenas, C., Obregón, M., Balbín, A., Villaveces, J. L., & Patarroyo, M. E. (2007). Wave function analysis of MHC-peptide interactions. Journal of Molecular Graphics and Modelling, 25(5), 605-615. https://doi.org/10.1016/j.jmgm.2006.04.005